In recent years, the research on plant nutrition has gained significant achievements in improving nutrient use efficiency in molecular plant nutrition, plant-microbe interaction, rhizosphere interaction, micro-ecological regulation, and nutrient management. However, how to coordinate food security, resource efficiency, and environmental sustainability to implement agriculture green development still confronts great challenges. Here, we propose a new concept of "Rhizobiont" and the corresponding working strategies to address this key issue. Aiming at the major scientific questions of "rhizosphere interaction and nutrient efficiency", the core thinking of this concept is to develop a systemic theory of the "Rhizobiont" consortium. This is an integrated system consisting of plants, roots, rhizosphere, hypersphere, and their associated microbes, and then to decipher the underlying mechanisms of plant-microbe and microbe-microbe interactions that drive high nutrient use efficiency. Specifically, the objectives, in theory, are to clarify the structure and function of rhizobiont consortium and their roles in the mobilization, uptake, and utilization of nutrients. Also, we seek to establish comprehensive management strategies for enhancing the biological potentials of the rhizobiont consortium via multi-interface interactions, allowing for a significant increase in crop productivity and nutrient use efficiency towards sustainable development. This new conceptual theory opens up an innovative research field of plant-soil-microbe interactions. Moreover, this concept seeks a comprehensive understanding of these interactions for harnessing the second genome of plants (microbiome), which will be the frontiers of agricultural research. The rhizobiont theory will help solve the problem of multi-objective coordination of food security, resource efficiency, and environmental protection. Thus, it provides scientific support for achieving agriculture green development in China. We further point out the key research contents and perspectives.